Computer Assisted Modeling

Contributions of Computational Approaches to Elucidating Macromolecular Structure and Function

Publisher: National Academies Press
ISBN: 9780309062282
eISBN Pdf: 9780309568296
Place of publication: United States
Year of digital publication: 1987
Month: January
Pages: 186
Language: English

COMPUTER-ASSISTED MODELING
Copyright
Preface
Contents
1. Executive Summary
- PROTEINS
  - Primary Structure
  - Predicting Secondary Structure from Amino Acid Sequences
  - Deriving Three-dimensional Structure and Function from Homology
  - Predicting Nucleic Acid Structures from Sequence
  - Tertiary Structure from X-ray Crystallography
  - Nuclear Magnetic Resonance
- TERTIARY STRUCTURE FROM THEORY
  - Energy Optimization
  - Homology
  - Molecular Dynamics
  - Thermodynamics
  - Solvent Effects
- ANALYSIS AND DESIGN OF DRUGS
- COMPLEX CARBOHYDRATES
  - ROLE OF COMPUTERS
- CONCLUSIONS
- RECOMMENDATIONS
2. Introduction
3. Primary Structure of Proteins and Nucleic Acids
- PROTEIN SEQUENCES AND DATA BASES
  - The Current Crystal Structure Census
  - Modeling on the Basis of Sequence Alone
  - Existing Data Bases
- PATTERN BASED COMPARISONS
  - Methodology
  - Software and Hardware Considerations
4. Secondary Structure of Proteins and Nucleic Acids
- PROTEINS
  - Current Status and Future Prospects
- NUCLEIC ACIDS
  - Predicting RNA Structure
  - Predicting DNA Structure
5. Tertiary Structure of Proteins and Nucleic Acids: Experimental
- X-RAY DIFFRACTION OF BIOLOGICAL MACROMOLECULES
- COMPUTER-ASSISTED MODELING IN DNA STRUCTURE ANALYSIS
  - Difference Patterson Vector Maps to Locate Heavy Atoms
  - Construction of a Trial Structure into an Electron Density Map
  - Display of Intermediate Maps for Checking Errors in the Structure
  - Location of Solvent Molecules and Ions Around a Macromolecule
  - Display of Completed Macromolecular Structure
  - Studies of Docking and Macromolecular Interactions
- USING NUCLEAR MAGNETIC RESONANCE TO DETERMINE TERTIARY STRUCTURES
  - Methodology
  - Viability of Approach
  - Limitations and Prospects for the Future
- AREAS OF POTENTIAL IMPACT OF NMR
  - Proteins and Peptides
  - Nucleic Acids
  - Carbohydrates
- DEMAND ON COMPUTATIONAL FACILITIES
6. Tertiary Structure of Proteins and Nucleic Acids: Theory
- ENERGY OPTIMIZATION
  - Generation of an Arbitrary Conformation
  - Potential Functions
  - Solvation
  - Entropy
  - Optimization Procedures
  - Solutions to the Multiple-Minima Problem for Macromolecules
  - Successes and Failures
  - Impediments to Progress
  - Future Prospects
  - MOLECULAR DYNAMICS
- RESULTS
  - The Determination of Macromolecular Structure
  - Spectroscopy/Kinetics and Molecular Dynamics
  - Thermodynamics of Macromolecules
  - Prognosis of Developments
- SOLVATION AND ELECTROSTATICS IN COMPUTER SIMULATION OF BIOPOLYMERS
  - All-Atom Modeling
  - Implicit Environmental Modeling
  - Conclusions
- HEURISTIC METHODS
  - Homology
  - Modeling by Extension
  - Exon Shuffling
- HIERARCHICAL MODELS OF PROTEIN FOLDING
- PATTERN RECOGNITION AND ARTIFICIAL INTELLIGENCE
7. Functional Aspects of Proteins and Nucleic Acids
- CATALYSIS
  - The Theory of Enzyme Catalysis
- DESIGNING NEW PROTEIN STRUCTURES
  - Computer Representation
  - Impediments to Progress
- PREDICTING FUNCTION FROM A PREDICTED THREE-DIMENSIONAL STRUCTURE
  - Experience in Ligand Design from Experimental Protein Structures
  - Experience in Ligand Design from Predicted Protein Structures
  - Inferring Binding Sites
  - Computer Tools for Ligand Design from Three-Dimensional Protein Structure
  - Impediments to Ligand Design from Protein Structures
8. Structure and Function of Complex Carbohydrates
- BIOLOGICAL FUNCTION
- BIOSYNTHESIS OF N-LINKED GLYCOPROTEINS AND GLYCOSPHINGOLIPIDS
- ANALYSIS OF PRIMARY AND TERTIARY STRUCTURE
- X-RAY ANALYSIS OF CRYSTAL STRUCTURES OF CARBOHYDRATES
- NMR SOLUTION STRUCTURES OF CARBOHYDRATES
- SUPRAMOLECULAR STRUCTURE
9. Hardware
- CENTRAL VERSUS DISTRIBUTED COMPUTING
- COMPUTER UTILIZATION IN THE NEXT 5 TO 10 YEARS
- THE NATIONAL SUPERCOMPUTER NETWORK
- LOCAL AREA NETWORKS
- DATA BASE USE
- COMPETITIVENESS
10. Conclusions and Recommendations
- CONCLUSIONS
- RECOMMENDATIONS
References